X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=6dacbd85a27238db065e0c1137c2de51aa4d9979;hb=d2dedc9e221d62b9320e38783d657fd2e4826709;hp=dcc3518e8e71ac354e7a7d33efb43464523bd5c8;hpb=24de2d6a6f3db1b9d55f367e2bf8ba112e202a8a;p=jalview.git diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index dcc3518..6dacbd8 100755 --- a/src/jalview/gui/Finder.java +++ b/src/jalview/gui/Finder.java @@ -20,23 +20,15 @@ */ package jalview.gui; -import jalview.api.AlignViewportI; -import jalview.api.FinderI; -import jalview.datamodel.SearchResultMatchI; -import jalview.datamodel.SearchResultsI; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.jbgui.GFinder; -import jalview.util.MessageManager; -import jalview.viewmodel.AlignmentViewport; - import java.awt.Dimension; import java.awt.event.ActionEvent; +import java.awt.event.FocusAdapter; +import java.awt.event.FocusEvent; import java.awt.event.KeyEvent; import java.util.ArrayList; import java.util.HashMap; import java.util.List; +import java.util.Locale; import java.util.Map; import java.util.regex.Pattern; import java.util.regex.PatternSyntaxException; @@ -49,6 +41,15 @@ import javax.swing.KeyStroke; import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; +import jalview.api.AlignViewportI; +import jalview.api.FinderI; +import jalview.datamodel.SearchResultMatchI; +import jalview.datamodel.SearchResultsI; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.jbgui.GFinder; +import jalview.util.MessageManager; + /** * Performs the menu option for searching the alignment, for the next or all * matches. If matches are found, they are highlighted, and the user has the @@ -66,7 +67,7 @@ public class Finder extends GFinder private static final int MIN_HEIGHT = 120; - private static final int MY_HEIGHT = 120; + private static final int MY_HEIGHT = 150; private static final int MY_WIDTH = 400; @@ -84,49 +85,62 @@ public class Finder extends GFinder private SearchResultsI searchResults; /* - * true if we only search a given alignment view - */ - private boolean focusfixed; - - /** - * Creates a new Finder object with no associated viewport or panel. Each Find - * or Find Next action will act on whichever viewport has focus at the time. + * true if Finder always acts on the same alignment, + * false if it acts on the alignment with focus */ - public Finder() - { - this(null, null); - } + private boolean focusFixed; /** - * Constructor given an associated viewport and alignment panel. Constructs - * and displays an internal frame where the user can enter a search string. + * Constructor given an associated alignment panel. Constructs and displays an + * internal frame where the user can enter a search string. The Finder may + * have 'fixed focus' (always act the panel for which it is constructed), or + * not (acts on the alignment that has focus). An optional 'scope' may be + * added to be shown in the title of the Finder frame. * - * @param viewport * @param alignPanel + * @param fixedFocus + * @param scope */ - public Finder(AlignmentViewport viewport, AlignmentPanel alignPanel) + public Finder(AlignmentPanel alignPanel, boolean fixedFocus, String scope) { - av = viewport; + av = alignPanel.getAlignViewport(); ap = alignPanel; + focusFixed = fixedFocus; finders = new HashMap<>(); - focusfixed = viewport != null; frame = new JInternalFrame(); frame.setContentPane(this); frame.setLayer(JLayeredPane.PALETTE_LAYER); - frame.addInternalFrameListener( - new InternalFrameAdapter() - { - @Override - public void internalFrameClosing(InternalFrameEvent e) - { - closeAction(); - } - }); + frame.addInternalFrameListener(new InternalFrameAdapter() + { + @Override + public void internalFrameClosing(InternalFrameEvent e) + { + closeAction(); + } + }); + frame.addFocusListener(new FocusAdapter() + { + @Override + public void focusGained(FocusEvent e) + { + /* + * ensure 'ignore hidden columns' is only enabled + * if the alignment with focus has hidden columns + */ + getFocusedViewport(); + } + }); + addEscapeHandler(); - Desktop.addInternalFrame(frame, MessageManager.getString("label.find"), - MY_WIDTH, MY_HEIGHT); + + String title = MessageManager.getString("label.find"); + if (scope != null) + { + title += " " + scope; + } + Desktop.addInternalFrame(frame, title, MY_WIDTH, MY_HEIGHT); frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); - searchBox.requestFocus(); + searchBox.getComponent().requestFocus(); } /** @@ -173,16 +187,18 @@ public class Finder extends GFinder /** * if !focusfixed and not in a desktop environment, checks that av and ap are * valid. Otherwise, gets the topmost alignment window and sets av and ap - * accordingly + * accordingly. Also sets the 'ignore hidden' checkbox disabled if the + * viewport has no hidden columns. * * @return false if no alignment window was found */ boolean getFocusedViewport() { - if (focusfixed || Desktop.desktop == null) + if (focusFixed || Desktop.desktop == null) { if (ap != null && av != null) { + ignoreHidden.setEnabled(av.hasHiddenColumns()); return true; } // we aren't in a desktop environment, so give up now. @@ -199,6 +215,7 @@ public class Finder extends GFinder { av = ((AlignFrame) alignFrame).viewport; ap = ((AlignFrame) alignFrame).alignPanel; + ignoreHidden.setEnabled(av.hasHiddenColumns()); return true; } } @@ -207,15 +224,19 @@ public class Finder extends GFinder /** * Opens a dialog that allows the user to create sequence features for the - * find match results. + * find match results */ @Override public void createFeatures_actionPerformed() { + if (searchResults.isEmpty()) + { + return; // shouldn't happen + } List seqs = new ArrayList<>(); List features = new ArrayList<>(); - String searchString = searchBox.getEditor().getItem().toString().trim(); + String searchString = searchBox.getUserInput(); String desc = "Search Results"; /* @@ -225,22 +246,42 @@ public class Finder extends GFinder for (SearchResultMatchI match : searchResults.getResults()) { seqs.add(match.getSequence().getDatasetSequence()); - features.add(new SequenceFeature(searchString, desc, - match - .getStart(), match.getEnd(), desc)); + features.add(new SequenceFeature(searchString, desc, match.getStart(), + match.getEnd(), desc)); } - if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs, - features, true, ap)) + new FeatureEditor(ap, seqs, features, true).showDialog(); + } + + @Override + protected void copyToClipboard_actionPerformed() + { + if (searchResults.isEmpty()) { - /* - * ensure feature display is turned on to show the new features, - * and remove them as highlighted regions - */ - ap.alignFrame.showSeqFeatures.setSelected(true); - av.setShowSequenceFeatures(true); - ap.highlightSearchResults(null); + return; // shouldn't happen } + List seqs = new ArrayList<>(); + + String searchString = searchBox.getUserInput(); + String desc = "Search Results"; + + /* + * assemble dataset sequences, and template new sequence features, + * for the amend features dialog + */ + for (SearchResultMatchI match : searchResults.getResults()) + { + SequenceI seq = match.getSequence(); + while (seq.getDatasetSequence() != null) + { + seq = seq.getDatasetSequence(); + } + seqs.add(seq.getSubSequence(seq.findIndex(match.getStart()), + seq.findIndex(match.getEnd()) + 1)); + } + Desktop.jalviewClipboard = new Object[] { + seqs.toArray(new SequenceI[0]), ap.av.getAlignment().getDataset(), + ap.av.getAlignment().getHiddenColumns() }; } /** @@ -252,8 +293,9 @@ public class Finder extends GFinder void doSearch(boolean doFindAll) { createFeatures.setEnabled(false); + copyToClipboard.setEnabled(false); - String searchString = searchBox.getUserInput().trim(); + String searchString = searchBox.getUserInput(); if (isInvalidSearchString(searchString)) { @@ -269,22 +311,23 @@ public class Finder extends GFinder /* * first time we've searched this viewport */ - finder = new jalview.analysis.Finder(av.getAlignment()); + finder = new jalview.analysis.Finder(av); finders.put(av, finder); } - SequenceGroup selectionGroup = av.getSelectionGroup(); boolean isCaseSensitive = caseSensitive.isSelected(); boolean doSearchDescription = searchDescription.isSelected(); + boolean doSearchfeatures = searchFeatures.isSelected(); + boolean skipHidden = ignoreHidden.isSelected(); if (doFindAll) { - finder.findAll(searchString, selectionGroup, isCaseSensitive, - doSearchDescription); + finder.findAll(searchString, isCaseSensitive, doSearchDescription, + doSearchfeatures, skipHidden); } else { - finder.findNext(searchString, selectionGroup, isCaseSensitive, - doSearchDescription); + finder.findNext(searchString, isCaseSensitive, doSearchDescription, + doSearchfeatures, skipHidden); } searchResults = finder.getSearchResults(); @@ -298,8 +341,11 @@ public class Finder extends GFinder else { createFeatures.setEnabled(true); + copyToClipboard.setEnabled(true); } + searchBox.updateCache(); + ap.highlightSearchResults(searchResults); // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or // 'SelectRegion' selection @@ -307,29 +353,33 @@ public class Finder extends GFinder { JvOptionPane.showInternalMessageDialog(this, MessageManager.getString("label.finished_searching"), null, - JvOptionPane.INFORMATION_MESSAGE); + JvOptionPane.PLAIN_MESSAGE); } else { if (doFindAll) { // then we report the matches that were found - String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs" - : ""; + StringBuilder message = new StringBuilder(); + if (idMatch.size() > 0) + { + message.append(idMatch.size()).append(" IDs"); + } if (searchResults != null) { - if (idMatch.size() > 0 && searchResults.getSize() > 0) + if (idMatch.size() > 0 && searchResults.getCount() > 0) { - message += " and "; + message.append(" ").append(MessageManager.getString("label.and") + .toLowerCase(Locale.ROOT)).append(" "); } - message += searchResults.getSize() - + " subsequence matches found."; + message.append(MessageManager.formatMessage( + "label.subsequence_matches_found", + searchResults.getCount())); } - JvOptionPane.showInternalMessageDialog(this, message, null, - JvOptionPane.INFORMATION_MESSAGE); + JvOptionPane.showInternalMessageDialog(this, message.toString(), + null, JvOptionPane.INFORMATION_MESSAGE); } } - searchBox.updateCache(); } /**